Applied Research section 2 ? Project Summary Following identification of associations between characteristics of a complex gut microbiota (GM) and resistance or susceptibility to disease, investigators frequently attempt to evaluate the causality of those associations by transferring the GM between resistant and susceptible animals. There are several ways to do so including embryo transfer of GM recipients into pseudopregnant GM donors, cross-fostering of neonatal GM recipients to nursing GM donors, simply co-housing animals, or experimentally administering a slurry prepared from donor feces to germ-free or antibiotic-treated GM recipients (fecal microbiota transfer, FMT). Whether successful or not in transferring the phenotype, few studies closely examine or report the efficiency of GM transfer from donor to recipient, and very few studies directly compare more than one method of GM transfer. Moreover, differences in the microbial diversity within donor and recipient GMs are known to influence the success of GM transfer. Thus the long-term objectives of Applied Research section 2 (Specific Aim 1) are to compare the efficiency of GM transfer using the aforementioned methods and well-controlled and thoroughly characterized GM recipients and donors harboring low and high-diversity GM profiles. Specific Aim 1 is to test the efficiency of GM transfer using embryo transfer, cross-fostering, co-housing, and FMT, in reciprocal transfers between low-diversity GM donors and high-diversity recipients and vice versa, and to determine whether the degree of GM transfer is associated with the degree to which the phenotype is also transferred. Furthermore, while feces represents a non-invasive sample allowing for longitudinal sampling of individual mice, it is well-recognized that feces reflects only the lower gastrointestinal tract (GIT). Many physiological processes and disease mechanisms are dependent on the GM present in the upper GIT, necessitating multiple terminal cohorts of mice for longitudinal studies as non-invasive ante mortem sampling of the upper GIT is not currently possible. With that in mind, the long-term objective of Applied Research section 2 (Specific Aim 2) is to develop and validate a system of non-invasively sampling the upper GIT for downstream sequencing methods. Working with a team of biomaterials engineers, Specific Aim 2 to develop a polymeric/metallic particle-based system capable of collecting bacterial cells selectively from the upper GIT following oral gavage, and then being retrieved and isolated from feces for downstream molecular analyses. The development of such a system would advance the three ?R?s of comparative medicine by reducing the required number of mice for longitudinal studies examining the upper GIT. Moreover, these methods would revolutionize human medicine and would be imminently patentable and likely to lead to subsequent funding via multiple mechanisms. Collectively, the Aims of Applied Research section 2 will significantly enhance the ability of researchers from a wide range of fields to manipulate the GM of laboratory mice in an informed manner, and to sample regions of the GIT that were previously inaccessible.